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EnzyControl: Adding Functional and Substrate-Specific Control for Enzyme Backbone Generation

Neural Information Processing Systems

Designing enzyme backbones with substrate-specific functionality is a critical challenge in computational protein engineering. Current generative models excel in protein design but face limitations in binding data, substrate-specific control, and flexibility for de novo enzyme backbone generation. To address this, we introduce EnzyBind, a dataset with 11,100 experimentally validated enzyme-substrate pairs specifically curated from PDBbind. Building on this, we propose EnzyControl, a method that enables functional and substrate-specific control in enzyme backbone generation. Our approach generates enzyme backbones conditioned on MSAannotated catalytic sites and their corresponding substrates, which are automatically extracted from curated enzyme-substrate data. At the core of EnzyControl is EnzyAdapter, a lightweight, modular component integrated into a pretrained motifscaffolding model, allowing it to become substrate-aware. A two-stage training paradigm further refines the model's ability to generate accurate and functional enzyme structures. Experiments show that our EnzyControl achieves the best performance across structural and functional metrics on EnzyBind and EnzyBench benchmarks, with particularly notable improvements of 13% in designability and 13% in catalytic efficiency compared to the baseline models.


MixSignGraph: ASign Sequence is Worth Mixed Graphs of Nodes

Neural Information Processing Systems

Recent advances in sign language research have benefited from CNN-based backbones, which are primarily transferred from traditional computer vision tasks (e.g., object detection, image recognition). However, these CNN-based backbones usually excel at extracting features like contours and texture, but may struggle with capturing sign-related features. To capture such sign-related features, SignGraph model extracts the cross-region sign features by building the Local Sign Graph (LSG) module and the Temporal Sign Graph (TSG) module. However, we emphasize that although capturing cross-region dependencies can improve sign language performance, it may degrade the representation quality of local regions. To mitigate this, we introduce MixSignGraph, which represents sign sequences as a group of mixed graphs for feature extraction. Specifically, besides the LSG module and TSG module that model the intra-frame and inter-frame cross-regions features, we design a simple yet effective Hierarchical Sign Graph (HSG) module, which enhances local region representations following the extraction of cross-region features, by aggregating the same-region features from different-granularity feature maps of a frame, i.e., to boost discriminative local features. In addition, to further improve the performance of gloss-free sign language task, we propose a simple yet counter-intuitive Text-based CTCPre-training (TCTC) method, which generates pseudo gloss labels from text sequences for model pre-training. Extensive experiments conducted on the current five sign language datasets demonstrate that MixSignGraph surpasses the most current models on multiple sign language tasks across several datasets, without relying on any additional cues.


SIFusion: AUnified Fusion Framework for Multi-granularity Arctic Sea Ice Forecasting

Neural Information Processing Systems

Arctic sea ice performs a vital role in global climate and has paramount impacts on both polar ecosystems and coastal communities. In the last few years, multiple deep learning based pan-Arctic sea ice concentration (SIC) forecasting methods have emerged and showcased superior performance over physics-based dynamical models. However, previous methods forecast SIC at a fixed temporal granularity, e.g.


Ditch the Denoiser: Emergence of Noise Robustness in Self-Supervised Learning from Data Curriculum

Neural Information Processing Systems

Self-Supervised Learning (SSL) has become a powerful solution to extract rich representations from unlabeled data. Yet, SSL research is mostly focused on clean, curated and high-quality datasets. As a result, applying SSL on noisy data remains a challenge, despite being crucial to applications such as astrophysics, medical imaging, geophysics or finance. In this work, we present a fully selfsupervised framework that enables noise-robust representation learning without requiring a denoiser at inference or downstream fine-tuning. Our method first trains an SSL denoiser on noisy data, then uses it to construct a denoised-tonoisy data curriculum (i.e., training first on denoised, then noisy samples) for pretraining a SSL backbone (e.g., DINOv2), combined with a teacher-guided regularization that anchors noisy embeddings to their denoised counterparts. This process encourages the model to internalize noise robustness. Notably, the denoiser can be discarded after pretraining, simplifying deployment. On ImageNet-1k with ViT-B under extreme Gaussian noise (ฯƒ = 255, SNR = 0.72 dB), our method improves linear probing accuracy by 4.8% over DINOv2, demonstrating that denoiser-free robustness can emerge from noise-aware pretraining.


1 Appendix 2 AMore Details

Neural Information Processing Systems

Score 0 4 (normal) is most common across cohorts, while score 3 (severe) is rare--especially in PD-GaM 5 and 3DGait, highlighting class imbalance challenges. BMCLab offers a balanced ON/OFF medication split, 7 while E-LC is skewed toward ON-medication. DNE includes healthy, Parkinsonian, and other disease 8 groups for broader contrastive training. Figure A.3 shows label distributions for FoG-related cohorts. This artifact likely stems from the unusual top-down perspective--different from the front15 facing or side views seen in WHAM's training data [1]. While motion encoder-based models may be 16 robust to such distortions, feature-based gait classifiers rely on precise kinematic measurements and 17 thus require carefully corrected input data. To correct this slope artifact, we perform a frame-wise 18 rigid alignment of the reconstructed SMPL skeleton using the Kabsch algorithm [2]. The goal is to 19 rotate each frame so that anatomical directions align with canonical coordinate axes (up, forward), 20 while preserving natural gait structure. This motion 28 vector is then projected onto the ground plane (xz-plane) and used as the walking axis. In frames where the sacrum displacement is less than 30 4mm--indicating near-stationary posture--we fall back on a proxy direction: the cross product of 31 the hip vector (left hip to right hip) and the vertical vector.


LoRATv2: Enabling Low-Cost Temporal Modeling in One-Stream Trackers

Neural Information Processing Systems

Transformer-based algorithms, such as LoRAT, have significantly enhanced objecttracking performance. However, these approaches rely on a standard attention mechanism, which incurs quadratic token complexity, making real-time inference computationally expensive. In this paper, we introduce LoRATv2, a novel tracking framework that addresses these limitations with three main contributions. First, LoRATv2 integrates frame-wise causal attention, which ensures full selfattention within each frame while enabling causal dependencies across frames, significantly reducing computational overhead. Moreover, key-value (KV) caching is employed to efficiently reuse past embeddings for further speedup.


Knowledge Insulating Vision-Language-Action Models: Train Fast, Run Fast, Generalize Better

Neural Information Processing Systems

Vision-language-action (VLA) models provide a powerful approach to training control policies for physical systems, such as robots, by combining end-to-end learning with transfer of semantic knowledge from web-scale vision-language model (VLM) training. However, the constraints of real-time control are often at odds with the design of VLMs: the most powerful VLMs have tens or hundreds of billions of parameters, presenting an obstacle to real-time inference, and operate on discrete tokens rather than the continuous-valued outputs that are required for controlling robots. To address this challenge, recent VLA models have used specialized modules for efficient continuous control, such as action experts or continuous output heads, which typically require adding new untrained parameters to the pretrained VLM backbone. While these modules improve real-time and control capabilities, it remains an open question whether they preserve or degrade the semantic knowledge contained in the pretrained VLM, and what effect they have on the VLA training dynamics. In this paper, we study this question in the context of VLAs that include a continuous diffusion or flow matching action expert, showing that naively including such experts significantly harms both training speed and knowledge transfer. We provide an extensive analysis of various design choices, their impact on performance and knowledge transfer, and propose a technique for insulating the VLM backbone during VLA training that mitigates this issue.


CAR-Flow: Condition-Aware Reparameterization Aligns Source and Target for Better Flow Matching

Neural Information Processing Systems

Conditional generative modeling aims to learn a conditional data distribution from samples containing data-condition pairs. For this, diffusion and flow-based methods have attained compelling results. These methods use a learned (flow) model to transport an initial standard Gaussian noise that ignores the condition to the conditional data distribution. The model is hence required to learn both mass transport and conditional injection. To ease the demand on the model, we propose Condition-Aware Reparameterization for Flow Matching (CAR-Flow) - a lightweight, learned shift that conditions the source, the target, or both distributions. By relocating these distributions, CAR-Flow shortens the probability path the model must learn, leading to faster training in practice. On low-dimensional synthetic data, we visualize and quantify the effects of CAR-Flow. On higher-dimensional natural image data (ImageNet-256), equipping SiT-XL/2 with CAR-Flow reduces FID from 2.07 to 1.68, while introducing less than 0.6% additional parameters.



Towards Implicit Aggregation: Robust Image Representation for Place Recognition in the Transformer Era

Neural Information Processing Systems

Visual place recognition (VPR) is typically regarded as a specific image retrieval task, whose core lies in representing images as global descriptors. Over the past decade, dominant VPR methods (e.g., NetVLAD) have followed a paradigm that first extracts the patch features/tokens of the input image using a backbone, and then aggregates these patch features into a global descriptor via an aggregator. This backbone-plus-aggregator paradigm has achieved overwhelming dominance in the CNN era and remains widely used in transformer-based models. In this paper, however, we argue that a dedicated aggregator is not necessary in the transformer era, that is, we can obtain robust global descriptors only with the backbone. Specifically, we introduce some learnable aggregation tokens, which are prepended to the patch tokens before a particular transformer block. All these tokens will be jointly processed and interact globally via the intrinsic self-attention mechanism, implicitly aggregating useful information within the patch tokens to the aggregation tokens.